A New Frontier

Mark Zylka never set out to find the neurological causes for autism. He cut his teeth studying chronic pain. But while collaborating on a project with UNC School of Medicine colleague Ben Philpot, Zylka serendipitously found that when specific brain enzymes are impaired, some of the genes implicated in autism are affected. So the big question for Zylka became: what can foul up those enzymes and potentially cause autism?

In his most recent paper, published in August in the journal Nature, Zylka’s team describes how certain chemotherapies inhibit the expression of a group of enzymes called topoisomerases. But topoisomerase-inhibitors are found in many places. No one knows if other environmental factors cause autism. But Zylka received a five-year, $3.8-million Pioneer Award from the National Institutes of Health to find out what role genetic and environmental factors might play.

Pioneer Awards are given to scientists who have stepped beyond their typical field of study to conduct research that could pave the way for treatments of major medical problems. Zylka, who came to the UNC School of Medicine in 2006, also won a Hettleman Prize for his work in autism and chronic pain.

We sat down with Dr. Zylka on September 26, the day he received his grant, to discuss how he started studying brain enzymes, the details and implications of his research, and what motivates him.

What was the driving force behind your majoring in biochemistry at Va. Tech and then getting a PhD in neurobiology at Harvard?

It started because of a high-school teacher who had an independent research class. We were learning about the nitrogen cycle and did real experiments. Typically, we wouldn’t have had a chance to do those kinds of experiments in a high school setting. That experience gave me the research bug. But I wasn’t sure what to major in. At the time, glowing tobacco plants were in the news, and I thought it would be fun to do some sort of genetic engineering or biochemistry-type work. So I went to Virginia Tech and majored in biochemistry. While there, I did undergrad research, studying organisms and enzymes that live in extreme environments, like vents of volcanoes.

But getting more research exposure required persistence. I applied to the NIH’s Intramural Research Training Program. I was rejected the first time I applied. However, I was accepted the following year and got to work with Dr. David Klein. He was studying the enzymes that make melatonin, a hormone that promotes sleep.

David Klein, it turned out, previously worked with Steve Reppert, a neuroscientist at Harvard who was studying circadian rhythms in animals. The two of them talked about what I was doing in the lab.

At this point, I realized I wanted to do research as a career, but still wasn’t sure if biochemistry or neuroscience was what I wanted to focus on. Since my background was really in biochemistry, I applied to a bunch of biochemistry departments and one neuroscience program—at Harvard—for graduate school. After interviewing at almost all of the schools I applied to, I realized my interests were more aligned with neuroscience. Fortunately, I got in (at Harvard). So that’s how I started studying neuroscience.

How did you get involved in basic autism research?

It was an unexpected consequence. Autism was not on my radar when I started my lab at UNC. Ben Philpot, right next door to me, was studying learning and memory. He and I have lunch almost every day. We’d hang out and talk about science; we’d come up with ideas. At one point, Ben started to study Angelman syndrome, a development disorder that is very debilitating to children. Kids with Angelman often can’t speak, have severe intellectual disabilities, and also have sensory abnormalities like altered pain perception. Chronic pain was the focus of my lab.

So Ben asked, “Why don’t you look at pain sensitivity in our animal models?” I did that and it got me hooked. Around that time, I introduced Ben to Bryan Roth [a pharmacologist in the UNC School of Medicine]. I knew Bryan had just purchased a sophisticated new high-content imager, because I had helped Bryan evaluate the device, and knew the device would be perfect for a screen Ben was planning. Ben was interested in screening for drugs that could turn the Angelman gene on. The screen was a success. From it, Ben and Bryan found topoisomerase inhibitors.

I then got involved to help with the mechanistic aspects—to figure out how these drugs work in neurons. That’s what ultimately led to this Pioneer Award, because in the process of trying to find out how topoisomerase inhibitors work, we found a potential unifying theory for autism.

Your lab, in collaboration with Ben Philpot’s, found that inhibiting those topoisomerases fouled up some genes associated with autism. Could you explain the significance of these findings?

Our study points towards major genetic and environmental contributions to autism. The significance will become very apparent soon. We have more interesting things to publish, hopefully soon.

There are a lot of things that came together in our research. Autism prevalence is on the rise, and people are doing lot of research to understand why. People with autism are having their genomes sequenced. And we can now link autism to genetic mutations and genes. Three hundred genes have been identified; mutations in these genes increase autism risk or cause the disease. Those 300 genes are from many different classes. Other researchers found that 15-20 percent of those genes are related to synapse formation and function. Synapses allow neurons to communicate with one another. So a number of these autism genes help neurons communicate.

Recently, researchers found a number of autism genes that are involved in transcriptional regulation—how genes are expressed. No one really understands how these genes relate to autism. If this is a brain disorder, what’s unique about these transcriptional processes? So that’s where this Nature paper and the Pioneer Award come in, because we made a couple of unexpected observations that link these concepts together.

First is that a lot of these synaptic genes are incredibly long. Genes occupy a certain amount of territory in the genome. On average, we found that autism genes are 5 times longer than other genes. And many are monsters—25 to 50 times longer than the average-size genes.

Well, we found that if you inhibit topoisomerases and then look at gene expression, most genes in the genome are not affected. But the really long genes are. This tied topoisomerases to the expression of really long genes. So, we recognized that drugs that inhibit topoisomerases affect really long genes. And we now realize that a lot of the really long genes are important in brain development.

This is where the unified theory comes from. If you mutate some of the genes that regulate transcriptional processes, these mutations could preferentially affect the expression of long genes, because long genes are more sensitive to problems with transcription. So, mutations in transcriptional regulators might affect longer genes to a greater extent, particularly the long genes that are involved in brain development. This is the idea we’re pursuing.

We know that certain chemotherapeutic drugs can inhibit topoisomerases. We studied that and published our findings in Nature. But there are other things that inhibit topoisomerases. We’re studying these other things to see if they have an impact on the genes linked with autism.

Another vein of research in your lab is chronic pain. What are some of your lab’s key findings and where does that work stand today?

That work is just as active as the autism work. My motivation to study pain stems from an urge to help people. And, the people who fund this work—the taxpayers—want to see a return at some level. And I do, too.

Fact is, more people suffer from chronic pain than heart disease, cancer, and diabetes combined. If you want to help a lot of people, then pain is the thing to go after. And it’s perfect for a neuroscientist, because it’s about the nervous system sending painful signals to the brain. If you regulate that activity, you can treat pain.

So I wanted to focus my lab on identifying new molecular targets that can be used to treat pain. We don’t do clinical studies in my lab but I’ve always been motivated to help people through my research. When I was a postdoc, we found a large family of G-protein coupled receptors. Drug companies love to target these receptors to treat diseases.

So our lab decided to move beyond opioids and NSAIDS [non-steroidal anti-inflammatory drugs] and find new things that regulate the excitability of pain-sensing neurons. Then I’d try to validate these new targets so that an outside biotech or drug company would become interested.

This strategy seems to be paying off. We found that PAP [a protein found in the body] could relieve pain and that a single injection [of purified PAP] lasts several days in animal models. Aerial BioPharma—a local biotech company—is developing a version for humans. Hopefully in the not too distant future people will be able to use PAP as an alternative to opioids.

And we have funding from NIH to work on a new class of lipid kinases that seem to be very effective at regulating pain. So we’re not shutting down pain research at all. It’s still half of our lab.

What is the most rewarding part of your job as a researcher?

Knowing that what I’m doing has the potential to help people down the road. We have a limited time on this planet and I want to do as much as I can during this time. I was trained to do cutting-edge neuroscience research, and I want to direct that knowledge and training toward helping people.

One of the things I’ve learned as a scientist is that the limitation is not what you can do but what your goal is. Setting the goal—framing what you want to accomplish—is critical.

So, if your goal is ambitious—to find new drugs to treat pain or to better understand the causes of autism—if you’re working toward that goal, then you’re going to make progress toward it. But if your goal is more modest, then you’ll make progress toward that more modest goal.

So we set ambitious goals in our lab. Even if we don’t achieve all of them, we think that our trajectory will lead to something useful down the road.

Mark Zylka is an associate professor in the Department of Cell Biology and Physiology in the School of Medicine. Read the release about Dr. Zylka's latest paper online here.